Safely access, visualize and manage your structural data

 
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Collaboration

  • Share structural knowledge and hypotheses with colleagues

  • Increase value of your work

  • Share views the way you see them

 
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Security & integrity

  • Keep your structural data safe and whole

  • Guarantee the access to your data in the long run

  • Make complex analysis reproducible

 
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Sustainable & simple integration

  • Get ready for future massive intake of structural information (X-ray, NMR, Cryo-EM, etc.)

  • Benefit from a flexible REST API

  • Export analyses and data to common data formats

 
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Support

  • Interact directly with 3decision experts & developers

  • Join the customer Slack community for discussions on functionality

WHAT CAN I DO IN 3DECISION?

Browse and analyze structural knowledge

  • Browse the structural database using proteins, pockets, and ligands as queries
  • Check the binding profile of the ligands in my pocket of interest across different structures but also on close related proteins.
  • Check the binding site variability among these structures in terms of binding site shape (residues in contact variation) and properties (druggability, volume, etc).
  • Visualize experimental annotations mapped over the sequence and over the structure (e.g. to check if there is some natural variation in the binding site that I should worry about)
  • Verify if a specific animal model is suitable for tests on my target (i.e. check for mutations in the binding site for the specific species)
  • Identify the differences in the binding site to exploit to increase the selectivity for target X compared to the related target Y. 
  • Identify what part of the molecule to modify to gain selectivity for target X.
  • Identify putative off-targets for a specific protein-ligand complex (i.e. search for proteins having a similar pocket, similar pocket sequence, similar binding ligands).
  • Search binding sites containing a sub-pocket of interest (currently in a beta version, still work in progress).
  • Run a sequence search to find suitable templates to build my homology model.

Create and test hypotheses

  • Generate ideas for lead or tool compounds in a new project (i.e. run the target profiling search and get a list of ligands from the potential off-targets to start off).
  • Generate new ideas by exploring and superposing similar binding sites with molecules bound.
  • Create and test hypotheses by docking molecules existing in other structures or by drawing them myself.
  • Test binding hypotheses I have generated elsewhere (e.g. with docking software).
  • Check if the protein-ligand interactions in my binding hypothesis already have been observed in other structures in the database.

Add my own knowledge

  • Annotate a sequence to add my personal notes.
  • Upload my homology models or docking poses to integrate them in the database.

Share

  • Save a particular state of the application and share it via a link with colleagues to further discuss the results.
  • Extract prepared structures  
  • Download superimposed structures and ligands to continue my analysis with other software.
 

Did you miss our webinar on How to maximize the value of your 3D Biomolecular structures? Watch the replay here!